| Contributors |
| Preface |
| Volumes in Series |
| Phase Response Curves: Elucidating the Dynamics of Coupled Oscillators / A. Granada ; R. M. Hennig ; B. Ronacher ; A. Kramer ; H. Herzel1： |
| Introduction |
| Estimation of Phase Response Curves / 2： |
| Specific Applications / 3： |
| Discussion / 4： |
| Acknowledgments / Appendix I： |
| References |
| Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways / Kalyan C. Vinnakota ; Fan Wu ; Martin J. Kushmerick ; Daniel A. Beard |
| Biochemical Conventions and Calculations |
| Application to Physiological Systems |
| Acknowledgment |
| Analytical Methods for the Retrieval and Interpretation of Continuous Glucose Monitoring Data in Diabetes / Boris Kovatchev ; Marc Breton ; William Clarke |
| Decomposition of Sensor Errors |
| Measures of Average Glycemia and Deviation from Target |
| Risk and Variability Assessment |
| Measures and Plots of System Stability / 5： |
| Time-Series-Based Prediction of Future BG Values / 6： |
| Conclusions / 7： |
| Analysis of Heterogeneity in Molecular Weight and Shape by Analytical Ultracentrifugation Using Parallel Distributed Computing / Borries Demeler ; Emre Brookes ; Luitgard Nagel-Steger |
| Methodology |
| Job Submission |
| Results |
| Discrete Stochastic Simulation Methods for Chemically Reacting Systems / Yang Cao ; David C. Samuels |
| The Chemical Master Equation |
| The Stochastic Simulation Algorithm |
| The Tau-Leaping Method |
| Measurement of Simulation Error |
| Software and Two Numerical Experiments |
| Conclusion |
| Analyses for Physiological and Behavioral Rhythmicity / Harold B. Dowse |
| Types of Biological Data and Their Acquisition |
| Analysis in the Time Domain |
| Analysis in the Frequency Domain |
| Time/Frequency Analysis and the Wavelet Transform |
| Signal Conditioning |
| Strength and Regularity of a Signal |
| A Computational Approach for the Rational Design of Stable Proteins and Enzymes: Optimization of Surface Charge-Charge Interactions / Katrina L. Schweiker ; George I. Makhatadze8： |
| Computational Design of Surface Charge-Charge Interactions |
| Experimental Verification of Computational Predictions |
| Closing Remarks |
| Efficient Computation of Confidence Intervals for Bayesian Model Predictions Based on Multidimensional Parameter Space / Amber D. Smith ; Alan Genz ; David M. Freiberger ; Gregory Belenky ; Hans P. A. Van Dongen |
| Height of the Probability Density Function at the Boundary of the Smallest Multidimensional Confidence Region |
| Approximating a One-Dimensional Slice of the Probability Density Function by Means of Normal Curve Spline Pieces |
| Locating the Boundary of the Smallest Multidimensional Confidence Region |
| Finding the Minimum and Maximum of the Prediction Model over the Confidence Region |
| An Application: Bayesian Forecasting of Cognitive Performance Impairment during Sleep Deprivation |
| 95% Confidence Intervals for Bayesian Predictions of Cognitive Performance Impairment during Sleep Deprivation |
| Appendix |
| Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pK<a/ Calculations and Titration Curve Fitting / Jens Erik Nielsen9： |
| Calculating the pH Dependence of Protein Characteristics |
| Setting up and Running a pKa/ Calculation |
| Analyzing the Results of a pKa/ Calculation |
| How Reliable Are Calculated pKa/ Values? |
| Predicting pH Activity Profiles |
| Decomposition Analysis |
| Predicting Protein Stability Profiles |
| Fitting pH Titration Curves, pH Activity Profiles, and pH Stability Profiles |
| Least Squares in Calibration: Weights, Nonlinearity, and Other Nuisances / Joel Tellinghuisen10： |
| Review of Least Squares |
| Experiment Design Using Vprior/-Numerical Illustrations |
| Evaluation and Comparison of Computational Models / Jay I. Myung ; Yun Tang ; Mark A. Pitt11： |
| Conceptual Overview of Model Evaluation and Comparison |
| Model Comparison Methods |
| Model Comparison at Work: Choosing between Protein Folding Models |
| Desegregating Undergraduate Mathematics and Biology - Interdisciplinary Instruction with Emphasis on Ongoing Biomedical Research / Raina Robeva12： |
| Course Description |
| Mathematical Algorithms for High-Resolution DNA Melting Analysis / Robert Palais ; Carl T. Wittwer13： |
| Extracting Melting Curves from Raw Fluorescence |
| Methods Used for Clustering and Classifying Melting Curves by Genotype |
| Methods Used for Modeling Melting Curves |
| Biomathematical Modeling of Pulsatile Hormone Secretion: A Historical Perspective / William S. Evans ; Leon S. Farhy ; Michael L. Johnson14： |
| Early Attempts to Identify and Characterize Pulsatile Hormone Release |
| Impact of Sampling Protocol and Pulse Detection Algorithm on Hormone Pulse Detection |
| Application of Deconvolution Procedures for the Identification and Characterization of Hormone Secretory Bursts |
| Limitations and Subsequent Improvements in Deconvolution Procedures |
| Evaluation of Pulsatile and Basal Hormone Secretion Using a Stochastic Differential Equations Model |
| Characterization of Regulation of Signal and Response Elements: Estimation of Approximate Entropy |
| Evaluation of Coupled Systems |
| Evaluation of Hormonal Networks with Feedback Interactions |
| Future Directions |
| AutoDecon: A Robust Numerical Method for the Quantification of Pulsatile Events / Lenore Pipes ; Paula P. Veldhuis ; Ralf Nass ; Michael O. Thorner15： |
| Methods |
| Modeling Fatigue over Sleep Deprivation, Circadian Rhythm, and Caffeine with a Minimal Performance Inhibitor Model / Patrick L. Benitez ; Gary H. Kamimori ; Thomas J. Balkin ; Alexander Greene16： |
| Author Index |
| Subject Index |
| Correlation Analysis: A Tool for Comparing Relaxation-Type Models to Experimental Data / Maurizio Tomaiuolo ; Joel Tabak ; Richard Bertram |
| Scatter Plots and Correlation Analysis |
| Example 1: Relaxation Oscillations |
| Example 2: Square Wave Bursting |
| Example 3: Elliptic Bursting |
| Example 4: Using Correlation Analysis on Experimental Data |
| Summary |
| Trait Variability of Cancer Cells Quantified by High-Content Automated Microscopy of Single Cells / Vito Quaranta ; Darren R. Tyson ; Shawn P. Garbett ; Brandy Weidow ; Mark P. Harris ; Walter Georgescu |
| Background |
| Experimental and Computational Workflow |
| Application to Traits Relevant to Cancer Progression |
| Matrix Factorization for Recovery of Biological Processes from Microarray Data / Andrew V. Kossenkov ; Michael F. Ochs |
| Overview of Methods |
| Application to the Rosetta Compendium |
| Results of Analyses |
| Modeling and Simulation of the Immune System as a Self-Regulating Network / Peter S. Kim ; Doron Levy ; Peter P. Lee |
| Mathematical Modeling of the Immune Network |
| Two Examples of Models to Understand T Cell Regulation |
| How to Implement Mathematical Models in Computer Simulations |
| Concluding Remarks |
| Acknowledgmentss |
| Entropy Demystified: The ôThermoö-dynamics of Stochastically Fluctuating Systems / Hong Qian |
| Energy |
| Entropy and ôThermoö-dynamics of Markov Processes |
| A Three-State Two-Cycle Motor Protein |
| Phosphorylation-Dephosphorylation Cycle1 Kinetics |
| Summary and Challenges |
| Effect of Kinetics on Sedimentation Velocity Profiles and the Role of Intermediates / John J. Correia ; P. Holland Alday ; Peter Sherwood ; Walter F. Stafford |
| ABCD Systems |
| Monomer-Tetramer Model |
| Algebraic Models of Biochemical Networks / Reinhard Laubenbacher ; Abdul Salam Jarrah |
| Computational Systems Biology |
| Network Inference |
| Reverse-Engineering of Discrete Models: An Example |
| High-Through put Computing in the Sciences / Mark Morgan ; Andrew Grimshaw |
| What is an HTC Application? |
| HTC Technologies |
| High-Throughput Computing Examples |
| Advanced Topics |
| Large Scale Transcriptome Data Integration Across Multiple Tissues to Decipher Stem Cell Signatures / Ghislain Bidaut ; Christian J. Stoeckert |
| Systems and Data Sources |
| Data Integration |
| Artificial Neural Network Training and Validation |
| Future Development and Enhancement Plans |
| DynaFit-A Software Package for Enzymology / Petr Kuzmiĉ |
| Equilibrium Binding Studies |
| Initial Rates of Enzyme Reactions |
| Time Course of Enzyme Reactions |
| General Methods and Algorithms |
| Discrete Dynamic Modeling of Cellular Signaling Networks / Réka Albert ; Rui-Sheng Wang |
| Cellular Signaling Networks |
| Boolean Dynamic Modeling |
| Variants of Boolean Network Models |
| Application Examples |
| Conclusion and Discussion |
| The Basic Concepts of Molecular Modeling / Akansha Saxena ; Diana Wong ; Karthikeyan Diraviyam ; David Sept |
| Homology Modeling |
| Molecular Dynamics |
| Molecular Docking |
| Deterministic and Stochastic Models of Genetic Regulatory Networks / Ilya Shmulevich ; John D. Aitchison |
| Boolean Networks |
| Differential Equation Models |
| Probabilistic Boolean Networks |
| Stochastic Differential Equation Models |
| Bayesian Probability Approach to ADHD Appraisal / Jennifer Kim Penberthy |
| Bayesian Probability Algorithm |
| The Value of Bayesian Probability Approach as a Meta-Analysis Tool |
| Discussion and Future Directions |
| Simple Stochastic Simulation / Maria J. Schilstra ; Stephen R. Martin |
| Understanding Reaction Dynamics |
| Graphical Notation |
| Reactions |
| Reaction Kinetics |
| Transition Firing Rules |
| Notes |
| Monte Carlo Simulation in Establishing Analytical Quality Requirements for Clinical Laboratory Tests: Meeting Clinical Needs / James C. Boyd ; David E. Bruns |
| Modeling Approach |
| Methods for Simulation Study |
| Nonlinear Dynamical Analysis and Optimization for Biological/Biomedical Systems / Amos Ben-Zvi ; Jong Mm Lee17： |
| Hypothalamic-Pituitary-Adrenal Axis System |
| Development of a Clinically Relevant Performance-Assessment Tools |
| Dynamic Programming |
| Computation of Optimal Treatments for HPA Axis System |
| Modeling of Growth Factor-Receptor Systems: From Molecular-Level Protein Interaction Networks to Whole-Body Compartment Models / Florence T. H. Wu ; Marianne O. Stefanini ; Feilim Mac Gabhann ; Aleksander S. Popel18： |
| Molecular-Level Kinetics Models: Simulation of In Vitro Experiments |
| Mesoscale Single-Tissue 3D Models: Simulation of In Vivo Tissue Regions |
| Single-Tissue Compartmental Models: Simulation at In Vivo Tissue |
| Multitissue Compartmental Models: Simulation of Whole Body |
| The Least-Squares Analysis of Data from Binding and Enzyme Kinetics Studies: Weights, Bias, and Confidence Intervals in Usual and Unusual Situations / 19： |
| Least Squares Review |
| Statistics of Reciprocals |
| Weights When y is a True Dependent Variable |
| Unusual Weighting: When x is the Dependent Variable |
| Assessing Data Uncertainty: Variance Function Estimation |
| Nonparametric Entropy Estimation Using Kernel Densities / Douglas E. Lake20： |
| Motivating Application: Classifying Cardiac Rhythms |
| Renyi Entropy and the Friedman-Tukey Index |
| Kernel Density Estimation |
| Mean-Integrated Square Error |
| Estimating the FT Index |
| Connection Between Template Matches and Kernel Densities |
| Summary and Future Work |
| Pancreatic Network Control of Glucagon Secretion and Counterregulation / Anthony L. McCall21： |
| Mechanisms of Glucagon Counterregulation (GCR) Dysregulation in Diabetes |
| Interdisciplinary Approach to Investigating the Defects in the GCR |
| Initial Qualitative Analysis of the GCR Control Axis |
| Mathematical Models of the GCR Control Mechanisms in STZ-Treated Rats |
| Approximation of the Normal Endocrine Pancreas by a Minimal Control Network (MCN) and Analysis of the GCR Abnormalities in the Insulin Deficient Pancreas |
| Advantages and Limitations of the Interdisciplinary Approach |
| Enzyme Kinetics and Computational Modeling for Systems Biology / Pedro Mendes ; Hanan Messiha ; Naglis Malys ; Stefan Hoops22： |
| Computational Modeling and Enzyme Kinetics |
| Yeast Triosephosphate Isomerase (EC 5.3.1.1) |
| Initial Rate Analysis |
| Progress Curve Analysis |
| Fitting Enzyme Kinetic Data with KinTek Global Kinetic Explorer / Kenneth A. Johnson23： |
| Challenges of Fitting by Simulation |
| Progress Curve Kinetics |
| Fitting Full Progress Curves |
| Slow Onset Inhibition Kinetics |
| Predicting Fluorescence Lifetimes and Spectra of Biopolymers / Patrik R. Callis |
| Modeling of Regulatory Networks: Theory and Applications in the study of the Drosophila Circadian Clock / Elizabeth Y. Scribner ; Hassan M. Fathallah-Shaykh |
| Strategies for articulated multibody-based adaptive coarse grain simulation of RNA / Mohammad Poursina ; Kishor D. Bhalerao ; Samuel C. Flores ; Kurt S. Anderson ; Alain Laederach |
| Modeling Loop Entropy / Gregory S. Chirikjian |
| Inferring Functional Relationships and Causal Network Structure from Gene Expression Profiles / Radhakrishnan Nagarajan |
| Numerical solution of the chemical master equation: uniqueness and stability of the stationary distribution for chemical networks, and mRNA bursting in a gene network with negative feedback regulation / E. S. Zeron ; M. Santill_an |
| How molecular should your molecular model be? On the level of molecular detail required to simulate biological networks in systems and synthetic biology / Didier Gonze ; Wassim Abou-Jaoud´e ; Adama Ouattara ; Jos´e Halloy |
| Computational modelling of biological pathways by executable biology / Maria Luisa Guerriero John K. Heath |
| Computing Molecular Fluctuations in Biochemical Reaction Systems Based on A Mechanistic, Statisitical Theory of Irreversible Processes / Don Kulasiri |
| Probing the input-output behaviour of biochemical and genetic systems: system identification methods from control theory / David McMillen ; Brian Ingalls ; Jordan Ang |
| Biochemical pathway modelling tools for drug target detection in cancer and other complex diseases / Alberto Marin-Sanguino ; Shailendra K. Gupta ; Eberhard O. Voit ; Julio Vera |
| Deterministic and Stochastic Simulation and Analysis of Biochemical Reaction Networks: The Lactose Operon Example / Necmettin Yildirim ; Caner Kazanci F. |
| Multivariate Neighborhood Sample Entropy: A method for data reduction and prediction of complex data / Joshua S. Richman MD, PhD |
| Scaling differences of heartbeat excursions between wake and sleep periods / L. Guzm´an-Vargas ; I. Reyes-Ram´irez ; R. Hern´andez-P´erez ; F. Angulo-Brown |
| Changepoint analysis for single-molecule polarized totalinternal reflection fluorescence microscopy experiments / John F. Beausang ; Yale E. Goldman ; Philip C. Nelson |
| Inferring mechanisms from dose-response curves / Carson C. Chow ; Karen M. Ong ; Edward J. Dougherty ; S. Stoney Simons, Jr |
| Spatial Aspects in Biological System Simulations / Haluk Resat ; Michelle N. Costa ; Harish Shankaran |
| Computational Approaches to Modeling Viral Structure and Assembly / Stephen C. Harvey ; Anton S. Petrov ; Batsal Devkota ; Mustafa Burak Boz |
| An Object-Oriented Software Suite for the Simulation and Design of Macromolecules / Andrew Leaver-Fay ; Michael Tyka ; Steven M. Lewis ; Oliver F. Lange ; James Thompson ; Ron Jacak ; Kristian Kaufman ; P. Douglas Renfrew ; Colin A. Smith ; Will Sheffler ; Ian W. Davis ; Seth Cooper ; Adrien Treuille ; Daniel J. Mandell ; Florian Richter ; Yih-En Andrew Ban ; Sarel J. Fleishman ; Jacob E. Corn ; David E. Kim ; Sergey Lyskov ; Monica Berrondo ; Stuart Mentzer ; Zoran Popovic ; James J. Havranek ; John Karanicolas ; Rhiju Das ; Jens Meiler ; Tanja Kortemme ; Jeffrey J. Gray ; Brian Kuhlman1 ; David Baker ; Philip Bradley |
| Computational Design of Intermolecular Stability and Specificity in Protein Self-Assembly / Vikas Nanda ; Sohail Zahid ; Fei Xu ; Daniel Levine |
